Presenter Status
Fellow
Abstract Type
Case Report
Primary Mentor or Principal Investigator
Laura Ramsey
Presentation Type
Oral Presentation
Start Date
13-5-2026 12:45 PM
End Date
13-5-2026 1:00 PM
Abstract Text
Background: Variants in the TPMT and NUDT15 genes that affect thiopurine metabolism can guide personalized dosing to minimize toxicity. Decreased or no appreciable NUDT15 activity demonstrate impaired breakdown of active thiopurine metabolites which can lead to severe adverse events including potentially life-threatening myelosuppression. Currently, the NUDT15*6 allele is classified as having uncertain function by the Clinical Pharmacogenetics Implementation Consortium due to insufficient data leading to indeterminate phenotype assignments.
Objectives/Goal: To describe the activity of the NUDT 15*6 allele.
Methods/Design: We present a pediatric patient with a NUDT15*1/*6 genotype who experienced significant thiopurine-induced myelosuppression. This patient was enrolled in the Children’s Mercy Research Institute Biorepository (Tumor Bank) study. The frequency of NUDT15*6 was determined in this cohort of patients with clinical short-read whole exome sequencing (srWES) data (n=339). Libraries for srWES were prepared with the Illumina TruSeq PCR-Free kit with 10 PCR cycles and enriched using the IDT xGen Exome Research Panel v2, then sequenced on a NovaSeq6000 platform to ≥300x targeted depth. Sequencing, primary analysis, alignment, and variant calling using DRAGEN v3.10.4 -v4.3.6 were performed by the Children’s Mercy Center for Genomic Medicine. The NUDT15 gene was filtered from the variant call files using BCFtoolsv1.18 (10) and star alleles were manually assigned based on PharmVar Nomenclature. The frequency of the NUDT15*6 allele was also calculated from participants enrolled in the Genomic Answers for Kids (GA4K) study. In the GA4K cohort, PacBio HiFi long-read sequencing (targeted coverage >25x) was used to identify and phase single nucleotide variants (SNVs) and structural variants using standard PacBio pipelines (pbmm2 v2.1.4.0, DeepVariant v1.0, WhatsHap v1.0, pbsv v2.4.0, and HIFI-CNV v1.0.1). NUDT15 star alleles were assigned with pb-StarPhase for subjects with a minimum of 10 reads, enabling accurate identification of the *1/*6 diplotype.
Results: The patient is a 4-year-old female with standard risk-average precursor B-cell acute lymphoblastic leukemia treated per AALL1731. Exome sequencing determined TPMT*1/*1 (normal metabolizer) and NUDT15*1/*6 (indeterminate metabolizer). After 75 mg/m2/day mercaptopurine, myelosuppression necessitated a three-week delay prior to the next phase of therapy. With 60 mg/m2/day thioguanine in a subsequent phase of therapy, she was admitted twice for fever and neutropenia. In the final phase of therapy, mercaptopurine at standard dosing of 75 mg/m2/day caused severe neutropenia and thrombocytopenia with elevated metabolite levels that required stopping mercaptopurine. After neutrophil recovery, a trial of 50% standard dosing was not tolerated and her dose was reduced to 27%, which was tolerated. Among 339 patients with cancer, sequencing revealed an allele frequency of 0.88% for NUDT15*6. In a larger cohort sequenced for suspicion of rare genetic disease, the frequency of NUDT15*6 was 0.15% among 1011 unrelated individuals.
Conclusions: This case demonstrates that a large dose reduction was necessary in a patient with TPMT *1/*1 and NUDT15 *1/*6, supporting the translation of this NUDT15 diplotype as intermediate metabolizer rather than indeterminate. Patients carrying NUDT15 *1/*6 should be closely monitored for thiopurine-related toxicities and may require significant dose reductions.
Severe Thiopurine-Induced Myelosuppression in a Pediatric Acute Lymphoblastic Leukemia Patient with the NUDT15 *1/*6 Genotype
Background: Variants in the TPMT and NUDT15 genes that affect thiopurine metabolism can guide personalized dosing to minimize toxicity. Decreased or no appreciable NUDT15 activity demonstrate impaired breakdown of active thiopurine metabolites which can lead to severe adverse events including potentially life-threatening myelosuppression. Currently, the NUDT15*6 allele is classified as having uncertain function by the Clinical Pharmacogenetics Implementation Consortium due to insufficient data leading to indeterminate phenotype assignments.
Objectives/Goal: To describe the activity of the NUDT 15*6 allele.
Methods/Design: We present a pediatric patient with a NUDT15*1/*6 genotype who experienced significant thiopurine-induced myelosuppression. This patient was enrolled in the Children’s Mercy Research Institute Biorepository (Tumor Bank) study. The frequency of NUDT15*6 was determined in this cohort of patients with clinical short-read whole exome sequencing (srWES) data (n=339). Libraries for srWES were prepared with the Illumina TruSeq PCR-Free kit with 10 PCR cycles and enriched using the IDT xGen Exome Research Panel v2, then sequenced on a NovaSeq6000 platform to ≥300x targeted depth. Sequencing, primary analysis, alignment, and variant calling using DRAGEN v3.10.4 -v4.3.6 were performed by the Children’s Mercy Center for Genomic Medicine. The NUDT15 gene was filtered from the variant call files using BCFtoolsv1.18 (10) and star alleles were manually assigned based on PharmVar Nomenclature. The frequency of the NUDT15*6 allele was also calculated from participants enrolled in the Genomic Answers for Kids (GA4K) study. In the GA4K cohort, PacBio HiFi long-read sequencing (targeted coverage >25x) was used to identify and phase single nucleotide variants (SNVs) and structural variants using standard PacBio pipelines (pbmm2 v2.1.4.0, DeepVariant v1.0, WhatsHap v1.0, pbsv v2.4.0, and HIFI-CNV v1.0.1). NUDT15 star alleles were assigned with pb-StarPhase for subjects with a minimum of 10 reads, enabling accurate identification of the *1/*6 diplotype.
Results: The patient is a 4-year-old female with standard risk-average precursor B-cell acute lymphoblastic leukemia treated per AALL1731. Exome sequencing determined TPMT*1/*1 (normal metabolizer) and NUDT15*1/*6 (indeterminate metabolizer). After 75 mg/m2/day mercaptopurine, myelosuppression necessitated a three-week delay prior to the next phase of therapy. With 60 mg/m2/day thioguanine in a subsequent phase of therapy, she was admitted twice for fever and neutropenia. In the final phase of therapy, mercaptopurine at standard dosing of 75 mg/m2/day caused severe neutropenia and thrombocytopenia with elevated metabolite levels that required stopping mercaptopurine. After neutrophil recovery, a trial of 50% standard dosing was not tolerated and her dose was reduced to 27%, which was tolerated. Among 339 patients with cancer, sequencing revealed an allele frequency of 0.88% for NUDT15*6. In a larger cohort sequenced for suspicion of rare genetic disease, the frequency of NUDT15*6 was 0.15% among 1011 unrelated individuals.
Conclusions: This case demonstrates that a large dose reduction was necessary in a patient with TPMT *1/*1 and NUDT15 *1/*6, supporting the translation of this NUDT15 diplotype as intermediate metabolizer rather than indeterminate. Patients carrying NUDT15 *1/*6 should be closely monitored for thiopurine-related toxicities and may require significant dose reductions.
